You can look this one up. See FY 09 budget request, justification materials, US Air Force, Aircraft procurement-Vol. 2, page 71.
You'll find on that page a detailed description for not one, but two potential mechanical problems that could cause a B-2A to crash.
Here's a sampling (read highlighted text):
The problem is caused by the B-2A's distorted engine inlets.
The distortion causes excessive wear on the stage 1 fan blades for the F118-GE-100 engines. Take that and an unplanned "foreign object damage event", and, voila, your $1.1 billion bomber may experience a "catastrophic in-flight emergency".
But there's another problem. A loose fan blade also can spark an "uncontained titanium fire". According to the same document, the titanium fire -- whatever that is -- may cause a "Class A event", or what normal people call a "crash".
The problem is listed in the budget justification documents because the USAF is buying repair blades this year to fix the problem. I'm sure it will be interesting for the investigators to find out whether the "Spirit of Kansas" had received the repairs before the crash, among other items of interest, of course.